simpleNucCall {ChIPseqR} | R Documentation |
This function provides a simplified interface to callBindingSites
with defaults suitable for
the detection of nucleosomes.
simpleNucCall(data, bind=128, support=17, background=2000, chrLen, ...)
data |
Either an object of class |
bind |
Length of binding region to use (see Details). |
support |
Length of support region to use (see Details). |
background |
Length of background window. If this is missing it will be set to 10*( |
chrLen |
Numeric vector indicating the length of all chromosomes. Only needed when
|
... |
Further arguments to |
A list
with components
binding |
A |
score |
A |
pval |
A |
Peter Humburg
~put references to the literature/web site here ~
callBindingSites
for additional parameters.
## generate some simple artificial read data set.seed(1) ## determine binding site locations b <- sample(1:1e6, 5000) ## sample read locations fwd <- unlist(lapply(b, function(x) sample((x-83):(x-73), 20, replace=TRUE))) rev <- unlist(lapply(b, function(x) sample((x+73):(x+83), 20, replace=TRUE))) ## add some background noise fwd <- c(fwd, sample(1:(1e6-25), 50000)) rev <- c(rev, sample(25:1e6, 50000)) ## create data.frame with read positions as input to strandPileup reads <- data.frame(chromosome="chr1", position=c(fwd, rev), length=25, strand=factor(rep(c("+", "-"), times=c(150000, 150000)))) ## create object of class ReadCounts readPile <- strandPileup(reads, chrLen=1e6, extend=1, plot=FALSE) ## predict binding site locations bindScore <- simpleNucCall(readPile, bind=147, support=20, plot=FALSE)